Planteome Ontology WG Zoom Meeting
- Date: Tuesday May. 24th, 2016
- Time: 8:15am PDT (GMT-7)
- Attendees: LC, AM, MAL, BS, EA, PJ
Agenda
- Planteome members attending: LC, MAL, AM, EA, GG, JD
Planteome Presentations:
- Monday afternoon: oral presentation (10 mins) LC: "The Planteome Project"
- Monday late afternoon: Poster presentation- LC, AM, MAL: Planteome Poster
- Tuesday morning: oral presentation (10 min)- AM: "Annotating germplasm using the Plant Trait Ontology in Planteome"
- Tuesday afternoon: oral presentation (10 min)- MAL: "Ontology Mapping Techniques for traits"
- Tuesday afternoon: Hands-on Session (2.5 hours)- LV:
- Progressing on the Trait Dictionaries: Groups: Tree species (cacao), Musa, barley, wheat, rice, sorghum, potato, sweet potato, yam
- Feedback on the TD template
- Leo is leaving the project as of May 30th- lack of funds and moving on to other things
- Continue work on TD, or is it dying?
- Julian taking a few crops over,
- EA, and MAL will be working on the remainder in their free time.
- Want to hire someone new, but no funds.
- several grants or something
Thursday afternoon: Hands-on Session (2.5 hours)-AM, LC: "Planteome: Bring Your Own Data Annotation Mini-Workshop
- 9 participants, 7 crop species:
- Nordine El- Hassouni - CIRAD - rice
- Trushar Shah- IITA, Kenya - cassava, cowpea, and banana
- Jeffery Detras - IRRI - rice
- Reinhard Simon - Centro Internacional de la Papa (CIP), Peru - potato/sweet potato
- Manuel Riuz - CIRAD, France / CIAT, Colombia - rice
- Cecile Grenier - CIRAD/CIAT Colombia - rice
- Ashley DuVal - Mars, Inc USA - cacao
- Anthony Bolger - RWTH Aachen University - Institute for Biology 1, Germany
- Astrid Junker - IPK Gatersleben, Germany - HTP phenotyping
- Outcomes:
- No matter how hard you try to streamline the process, the uniqueness of people's data will continue to require expert intervention.
- the work is never truly "automated", everything requires a human checkpoint.
- reference ontology space makes it very difficult to standardize workflow
- no one is an expert on all things we attempt to capture
- collaborating with other application ontologies or working groups is necessary
- High throughput phenotyping requires an entirely new standard vocabulary
- perhaps could be captured with a new set of "methods"?
- Only a few measurements are taken
- most of the "traits" are calculations and inferences
Discussion from meeting:
- Data sets with multiple reps of measurements- How do we capture this?
- single germplasm annotation with stable phenotypes
- multiple reps and/or multiple experiments
- GO - gaf2 has no way of capturing that
- TASSEL scheme or database schema would handle this??
- limit on our side
- new evidence code to associate genotype and phenotype
- experiment average of reps, average of locations
- column 16 - new relationship - tells users that the score was averaged somehow
- MAL sent a rice data set from Cecile Grenier (CIRAD/CIAT Colombia) which contains replicated data measurements
2. Planning for ICBO/BioCreative Conference
- BS will arrive the day before, and leave early on Friday
- Currently have 67 submissions, but only 12 people have registered
- PJ will send a reminder to the authors of the submitted papers:
- 1. In order to have your accepted submission included in the proceedings of the meeting, at least one author from each paper must register for the meeting.
- 2. Where authors are involved in more than one submission, a distinct author must register for each accepted paper.
- good to have a number of people to support the workshops
- Plant Biodiversity Workshop
- Title: Tools and Applications for Data Standards and Knowledge Sharing in Plant Biodiversity
- Workshop type: Project Workshop (Project specific talks + Discussions)
- Organizer: Laurel Cooper, Oregon State University
- Co-organizer(s): Dennis Wm. Stevenson, Chelsea Specht, Marie-Angelique LaPorte
3. Planning for Post-ICBO Curator Workshop
- The idea is this would be similar to the one held at OSU in November 2015
- Proposed Dates: Three days: Monday Aug 8th to Weds Aug 10th
- People can come for the ICBO meeting and then stay for the plant-specific, more hand's on session
- incentives:
- People have to stay through the weekend- we can pay for the stay in the dorms
- If they come to this meeting, we can pay for their ICBO registration.
- Who is interested in attending?- Ideally 5-6 people
- Indian guy - working to get TO terms added, rice gene annotations
- PJ will send LC
- Target wheat and maize researchers, primarily from CIMMYT ?, also rice
- Rosemary -wheat
- Julian Pietragalla- IBP , Mexico
- Kate - maize data manager
- Should we send out a survey?
- If people come for the week of ICBO, are they able to stay for an additional 5 days to a week?
- Other options: Perhaps do in September before OSU starts?
4.Planteome Ontology Updates
- "Soft Release" of Plant Ontology, still working out a few issues for the Plant Trait Ontology
Upcoming Meetings and Workshops
9th International Conference on Formal Ontology in Information Systems (FOIS 2016), Annecy, France on July 6th-9th, 2016
- BS is attending
- most technically sophisticated ontology meeting, non computational
- what relations should we use, how are ontologies taught?, what an object is?
- High level ontology design and engineering
- Planteome could present results in 2018, when we have some results - held every two years
- Dates: July 8th and 9th, with July 9th being the “Phenotype Day”, focused on the systematic description of phenotypes.
- Short papers, up to 4 pages (will be published in JBMS)
- Poster abstracts, up to 1 page
- Flash updates, up to 1 page